Nucleic acid sequence data is valuable in myriad applications in biological research and molecular medicine, including determining the hereditary factors in disease, in developing new methods to detect disease and guide therapy (van de Vijver et al. (2002) “A gene-expression signature as a predictor of survival in breast cancer,” New England Journal of Medicine 347: 1999-2009), and in providing a rational basis for personalized medicine. Obtaining and verifying sequence data for use in such analyses has made it necessary for sequencing technologies to undergo advancements to expand throughput, lower reagent and labor costs and improve accuracy (See, e.g., Chan, et al. (2005) “Advances in Sequencing Technology” (Review) Mutation Research 573: 13-40, Levene et al. (2003) “Zero Mode Waveguides for Single Molecule Analysis at High Concentrations,” Science 299: 682-686).
Current methods for preparing nucleic acid templates are not optimal for use in high throughput DNA sequencing systems, especially those that determine nucleotide sequences from single molecules of a template. Conventional cloning and cell culture methods are time consuming and expensive. Lengthy nucleic acid purification protocols currently in use do not reliably produce nucleic acid samples that are sufficiently free of sequencing reaction inhibitors such as salts, carbohydrates and/or proteins. Methods that utilize amplification introduce errors into the resulting amplicons that can be difficult to distinguish from true variants in the original sample. Furthermore, these problems are magnified when such conventional techniques are scaled to the quantities that would be useful for high throughput sequencing technologies. Consequently, there is an increasing demand for efficient, low-cost methods for the preparation of high-quality nucleic acid templates. In particular, such templates should either be error-free, or be amplified in such a way that any errors introduced during the amplification (or other steps of the template preparation) are distinguishable from genetic variants originally present in the sample nucleic acid. The present invention provides methods and compositions that would be useful for supplying high throughput DNA sequencing systems with such templates.